data_17786 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of the duplex when (5'S)-8,5'-cyclo-2'-deoxyguanosine is placed opposite dT ; _BMRB_accession_number 17786 _BMRB_flat_file_name bmr17786.str _Entry_type original _Submission_date 2011-07-18 _Accession_date 2011-07-18 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Huang Hai . . 2 Das Rajat S. . 3 Basu Ashis . . 4 Stone Michael P. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 167 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-06-25 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 17787 (5'S)-8,5'-cyclo-2'-deoxyguanosine 17788 'gamma-hydroxy-1,N2-propano-2'-deoxyguanosine adduct' 17789 (5'S)-8,5'-cyclo-2'-deoxyadenosine 17790 '(6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct' 17791 '(6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structures of (5'S)-8,5'-Cyclo-2'-deoxyguanosine Mismatched with dA or dT' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22309170 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Huang Hai . . 2 Das Rajat S. . 3 Basu Ashis . . 4 Stone Michael P. . stop_ _Journal_abbreviation 'Chem. Res. Toxicol.' _Journal_volume 25 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 478 _Page_last 490 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name (5'S)-8,5'-cyclo-2'-deoxyguanosine _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3')' $DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') 'DNA (5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-3')' $DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3')_ _Molecular_mass 2752.830 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence GTGCGTGTTTGT loop_ _Residue_seq_code _Residue_label 1 DG 2 DT 3 DG 4 DC 5 DG 6 DT 7 DG 8 DT 9 DT 10 DT 11 DG 12 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-3')_ _Molecular_mass 3022.044 _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence ACAAACATGCAC loop_ _Residue_seq_code _Residue_label 1 DA 2 DC 3 DA 4 DA 5 DA 6 DC 7 DA 8 DT 9 DG 10 DC 11 DA 12 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') . . . . . . $DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-3') . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') 'chemical synthesis' . . . . . $DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-3') 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') 1.0 mM 'natural abundance' $DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-3') 1.0 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 10 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 7.0 . pH pressure 1 . atm 'ionic strength' 100 . mM stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio water H 1 protons ppm 4.773 internal direct . . . 1.000000000 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA (5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3')' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 DG H1' H 6.060 .003 . 2 1 1 DG H2' H 2.695 .003 . 3 1 1 DG H2'' H 2.845 .003 2 4 1 1 DG H3' H 4.863 .003 . 5 1 1 DG H4' H 4.274 .003 . 6 1 1 DG H8 H 7.996 .003 1 7 2 2 DT H1' H 6.011 .003 . 8 2 2 DT H2' H 2.234 .003 . 9 2 2 DT H2'' H 2.591 .003 2 10 2 2 DT H3' H 4.966 .003 . 11 2 2 DT H4' H 4.299 .003 . 12 2 2 DT H6 H 7.409 .003 1 13 2 2 DT H71 H 1.429 .003 . 14 2 2 DT H72 H 1.429 .003 . 15 2 2 DT H73 H 1.429 .003 . 16 3 3 DG H1' H 5.954 .003 . 17 3 3 DG H2' H 2.614 .003 . 18 3 3 DG H2'' H 2.801 .003 2 19 3 3 DG H3' H 5.023 .003 . 20 3 3 DG H4' H 4.404 .003 . 21 3 3 DG H8 H 7.894 .003 1 22 4 4 DC H1' H 6.011 .003 . 23 4 4 DC H2' H 2.241 .003 . 24 4 4 DC H2'' H 3.273 .003 2 25 4 4 DC H3' H 4.996 .003 . 26 4 4 DC H4' H 4.392 .003 . 27 4 4 DC H5 H 5.514 .003 1 28 4 4 DC H6 H 7.555 .003 1 29 5 5 DG H1' H 6.114 .003 . 30 5 5 DG H2' H 2.254 .003 . 31 5 5 DG H3' H 4.918 .003 . 32 5 5 DG H4' H 5.200 .003 . 33 5 5 DG H5' H 5.553 .003 . 34 6 6 DT H1' H 6.014 .003 . 35 6 6 DT H2' H 2.279 .003 . 36 6 6 DT H2'' H 2.625 .003 2 37 6 6 DT H3' H 4.922 .003 . 38 6 6 DT H4' H 4.286 .003 . 39 6 6 DT H6 H 7.503 .003 1 40 6 6 DT H71 H 1.537 .003 . 41 6 6 DT H72 H 1.537 .003 . 42 6 6 DT H73 H 1.537 .003 . 43 7 7 DG H1' H 6.057 .003 . 44 7 7 DG H2' H 2.632 .003 . 45 7 7 DG H2'' H 2.846 .003 2 46 7 7 DG H3' H 4.986 .003 . 47 7 7 DG H4' H 4.408 .003 . 48 7 7 DG H8 H 7.850 .003 1 49 8 8 DT H1' H 6.098 .003 . 50 8 8 DT H2' H 2.186 .003 . 51 8 8 DT H2'' H 2.633 .003 2 52 8 8 DT H3' H 4.915 .003 . 53 8 8 DT H4' H 4.300 .003 . 54 8 8 DT H6 H 7.296 .003 1 55 8 8 DT H71 H 1.362 .003 . 56 8 8 DT H72 H 1.362 .003 . 57 8 8 DT H73 H 1.362 .003 . 58 9 9 DT H1' H 6.165 .003 . 59 9 9 DT H2' H 2.195 .003 . 60 9 9 DT H2'' H 2.635 .003 2 61 9 9 DT H3' H 4.930 .003 . 62 9 9 DT H4' H 4.211 .003 . 63 9 9 DT H6 H 7.486 .003 1 64 9 9 DT H71 H 1.648 .003 . 65 9 9 DT H72 H 1.648 .003 . 66 9 9 DT H73 H 1.648 .003 . 67 10 10 DT H1' H 5.879 .003 . 68 10 10 DT H2' H 2.017 .003 . 69 10 10 DT H2'' H 2.412 .003 2 70 10 10 DT H3' H 4.930 .003 . 71 10 10 DT H4' H 4.162 .003 . 72 10 10 DT H6 H 7.337 .003 1 73 10 10 DT H71 H 1.750 .003 . 74 10 10 DT H72 H 1.750 .003 . 75 10 10 DT H73 H 1.750 .003 . 76 11 11 DG H1' H 6.107 .003 . 77 11 11 DG H2' H 2.748 .003 . 78 11 11 DG H3' H 5.038 .003 . 79 11 11 DG H4' H 4.438 .003 . 80 11 11 DG H8 H 8.006 .003 1 81 12 12 DT H1' H 6.284 .003 . 82 12 12 DT H2' H 2.291 .003 . 83 12 12 DT H3' H 4.581 .003 . 84 12 12 DT H4' H 4.128 .003 . 85 12 12 DT H6 H 7.468 .003 1 86 12 12 DT H71 H 1.675 .003 . 87 12 12 DT H72 H 1.675 .003 . 88 12 12 DT H73 H 1.675 .003 . stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA (5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-3')' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 13 1 DA H1' H 6.206 .003 . 2 13 1 DA H2' H 2.620 .003 . 3 13 1 DA H2'' H 2.780 .003 2 4 13 1 DA H3' H 4.857 .003 . 5 13 1 DA H4' H 4.265 .003 . 6 13 1 DA H8 H 8.212 .003 1 7 14 2 DC H1' H 5.173 .003 . 8 14 2 DC H2' H 2.023 .003 . 9 14 2 DC H2'' H 2.251 .003 2 10 14 2 DC H3' H 4.806 .003 . 11 14 2 DC H4' H 4.114 .003 . 12 14 2 DC H5 H 5.525 .003 1 13 14 2 DC H6 H 7.432 .003 1 14 15 3 DA H1' H 5.793 .003 . 15 15 3 DA H2' H 2.768 .003 . 16 15 3 DA H2'' H 2.867 .003 2 17 15 3 DA H3' H 5.072 .003 . 18 15 3 DA H4' H 4.394 .003 . 19 15 3 DA H8 H 8.232 .003 1 20 16 4 DA H1' H 5.907 .003 . 21 16 4 DA H2' H 2.679 .003 . 22 16 4 DA H2'' H 2.887 .003 2 23 16 4 DA H3' H 5.090 .003 . 24 16 4 DA H4' H 4.473 .003 . 25 16 4 DA H8 H 8.143 .003 1 26 17 5 DA H1' H 6.072 .003 . 27 17 5 DA H2' H 2.572 .003 . 28 17 5 DA H2'' H 2.861 .003 2 29 17 5 DA H3' H 5.021 .003 . 30 17 5 DA H4' H 4.471 .003 . 31 17 5 DA H8 H 8.067 .003 1 32 18 6 DC H1' H 5.608 .003 . 33 18 6 DC H2' H 1.850 .003 . 34 18 6 DC H2'' H 2.329 .003 2 35 18 6 DC H3' H 4.765 .003 . 36 18 6 DC H4' H 4.147 .003 . 37 18 6 DC H5 H 5.167 .003 1 38 18 6 DC H6 H 7.094 .003 1 39 19 7 DA H1' H 6.157 .003 . 40 19 7 DA H2' H 2.422 .003 . 41 19 7 DA H2'' H 2.706 .003 2 42 19 7 DA H3' H 4.892 .003 . 43 19 7 DA H4' H 4.359 .003 . 44 19 7 DA H8 H 7.851 .003 1 45 20 8 DT H1' H 5.022 .003 . 46 20 8 DT H2' H 1.970 .003 . 47 20 8 DT H2'' H 2.045 .003 2 48 20 8 DT H3' H 4.781 .003 . 49 20 8 DT H4' H 3.897 .003 . 50 20 8 DT H6 H 7.155 .003 1 51 20 8 DT H71 H 1.894 .003 . 52 20 8 DT H72 H 1.894 .003 . 53 20 8 DT H73 H 1.894 .003 . 54 21 9 DG H1' H 5.864 .003 . 55 21 9 DG H2' H 2.614 .003 . 56 21 9 DG H2'' H 2.691 .003 2 57 21 9 DG H3' H 4.952 .003 . 58 21 9 DG H4' H 4.350 .003 . 59 21 9 DG H8 H 7.819 .003 1 60 22 10 DC H1' H 5.725 .003 . 61 22 10 DC H2' H 2.115 .003 . 62 22 10 DC H2'' H 2.441 .003 2 63 22 10 DC H3' H 4.870 .003 . 64 22 10 DC H4' H 4.214 .003 . 65 22 10 DC H5 H 5.335 .003 1 66 22 10 DC H6 H 7.382 .003 1 67 23 11 DA H1' H 6.305 .003 . 68 23 11 DA H2' H 2.715 .003 . 69 23 11 DA H2'' H 2.916 .003 2 70 23 11 DA H3' H 5.046 .003 . 71 23 11 DA H4' H 4.433 .003 . 72 23 11 DA H8 H 8.288 .003 1 73 24 12 DC H1' H 6.147 .003 . 74 24 12 DC H2' H 2.144 .003 . 75 24 12 DC H2'' H 2.171 .003 2 76 24 12 DC H3' H 4.516 .003 . 77 24 12 DC H4' H 4.071 .003 . 78 24 12 DC H5 H 5.454 .003 1 79 24 12 DC H6 H 7.428 .003 1 stop_ save_